omicverse.alignment.count

omicverse.alignment.count(index_path, t2g_path, technology, fastq_paths, output_path='.', whitelist_path=None, replacement_path=None, threads=8, memory='2G', workflow='standard', overwrite=False, temp_dir='tmp', tcc=False, mm=False, filter_barcodes=False, filter_threshold=None, loom=False, loom_names=None, h5ad=False, cellranger=False, gene_names=False, report=False, strand=None, parity=None, fragment_l=None, fragment_s=None, bootstraps=None, em=False, aa=False, genomebam=False, inleaved=False, batch_barcodes=False, exact_barcodes=False, numreads=None, store_num=False, long_read=False, threshold=0.8, platform='ONT', c1=None, c2=None, nucleus=False, **kwargs)[source]

Quantify expression matrices from FASTQ files via kb count.

Parameters:

  • index_path (str) – Path to kallisto index produced by kb ref.

  • t2g_path (str) – Transcript-to-gene mapping table used for gene-level aggregation.

  • technology (str) – Sequencing technology preset (for example 10XV3, BULK).

  • fastq_paths (str|list[str]) – One or more FASTQ file paths passed to kb count.

  • output_path (str, optional) – Output directory for count matrices and intermediate files.

  • whitelist_path (str|None, optional) – Optional custom barcode whitelist.

  • replacement_path (str|None, optional) – Optional barcode replacement file.

  • threads (int, optional) – Number of threads used by kb.

  • memory (str, optional) – Memory request string passed to kb (for example 2G).

  • workflow (str, optional) – kb workflow mode (standard, nucleus, lamanno etc.).

  • overwrite (bool, optional) – Whether to overwrite existing output directory contents.

  • temp_dir (str, optional) – Temporary directory root for kb intermediate files.

  • tcc (bool, optional) – Output transcript compatibility counts instead of gene matrix.

  • mm (bool, optional) – Use memory-mapped mode when supported.

  • filter_barcodes (bool, optional) – Enable barcode filtering (not valid for technology='BULK').

  • filter_threshold (int|None, optional) – Barcode filter threshold used by bustools filtering.

  • loom (bool, optional) – Export loom matrix.

  • loom_names (str|list[str]|None, optional) – Custom loom row/column naming behavior.

  • h5ad (bool, optional) – Export H5AD matrix output.

  • cellranger (bool, optional) – Emit Cell Ranger-compatible output structure.

  • gene_names (bool, optional) – Prefer gene symbols over IDs when possible.

  • report (bool, optional) – Generate additional kb report files.

  • strand (str|None, optional) – Strand option for long-read/technology-specific modes.

  • parity (str|None, optional) – Read parity setting for specific technologies.

  • fragment_l (int|None, optional) – Mean fragment length for bulk-like protocols.

  • fragment_s (int|None, optional) – Fragment length standard deviation.

  • bootstraps (int|None, optional) – Number of kallisto bootstrap rounds.

  • em (bool, optional) – Enable EM optimization.

  • aa (bool, optional) – Enable amino-acid mode where supported.

  • genomebam (bool, optional) – Request genome BAM generation (version-dependent support).

  • inleaved (bool, optional) – Treat reads as interleaved input.

  • batch_barcodes (bool, optional) – Enable batched barcode handling.

  • exact_barcodes (bool, optional) – Require exact barcode matching.

  • numreads (int|None, optional) – Limit number of reads processed.

  • store_num (bool, optional) – Store BUS record counts in output metadata.

  • long_read (bool, optional) – Enable long-read mode.

  • threshold (float, optional) – Long-read assignment threshold.

  • platform (str, optional) – Long-read platform label (for example ONT).

  • c1 (str|None, optional) – Spliced capture file path for velocity workflows.

  • c2 (str|None, optional) – Intronic capture file path for velocity workflows.

  • nucleus (bool, optional) – Shortcut to switch workflow from standard to nucleus.

  • **kwargs – Extra kb flags forwarded verbatim.

Returns:

Metadata dictionary including workflow settings and discovered output files.

Return type:

dict[str,str]